Direct prediction of carbapenem resistance in Pseudomonas aeruginosa by whole genome sequencing and metagenomic sequencing

铜绿假单胞菌 碳青霉烯 美罗培南 亚胺培南 基因组 微生物学 生物 基因型 抗生素耐药性 基因 抗生素 细菌 遗传学 医学 肺结核 病理
作者
Bing Liu,Jianpeng Gao,Xue Fei Liu,Guanhua Rao,Jiajie Luo,Han Peng,Weiting Hu,Ze Zhang,Qianqian Zhao,Lizhong Han,Zhi Jiang,Min Zhou
出处
期刊:Journal of Clinical Microbiology [American Society for Microbiology]
卷期号:61 (11) 被引量:6
标识
DOI:10.1128/jcm.00617-23
摘要

ABSTRACT Carbapenem resistance is a major concern in the management of antibiotic-resistant Pseudomonas aeruginosa infections. The direct prediction of carbapenem-resistant phenotype from genotype in P. aeruginosa isolates and clinical samples would promote timely antibiotic therapy. The complex carbapenem resistance mechanism and the high prevalence of variant-driven carbapenem resistance in P. aeruginosa make it challenging to predict the carbapenem-resistant phenotype through the genotype. In this study, using whole genome sequencing (WGS) data of 1,622 P . aeruginosa isolates followed by machine learning, we screened 16 and 31 key gene features associated with imipenem (IPM) and meropenem (MEM) resistance in P. aeruginosa , including oprD(HIGH), and constructed the resistance prediction models. The areas under the curves of the IPM and MEM resistance prediction models were 0.906 and 0.925, respectively. For the direct prediction of carbapenem resistance in P. aeruginosa from clinical samples by the key gene features selected and prediction models constructed, 72 P . aeruginosa -positive sputum samples were collected and sequenced by metagenomic sequencing (MGS) based on next-generation sequencing (NGS) or Oxford Nanopore Technology (ONT). The prediction applicability of MGS based on NGS outperformed that of MGS based on ONT. In 72 P . aeruginosa -positive sputum samples, 65.0% (26/40) of IPM-insensitive and 63.2% (24/38) of MEM-insensitive P. aeruginosa were directly predicted by NGS-based MGS with positive predictive values of 0.897 and 0.889, respectively. By the direct detection of the key gene features associated with carbapenem resistance of P. aeruginosa , the carbapenem resistance of P. aeruginosa could be directly predicted from cultured isolates by WGS or from clinical samples by NGS-based MGS, which could assist the timely treatment and surveillance of carbapenem-resistant P. aeruginosa .
最长约 10秒,即可获得该文献文件

科研通智能强力驱动
Strongly Powered by AbleSci AI
更新
PDF的下载单位、IP信息已删除 (2025-6-4)

科研通是完全免费的文献互助平台,具备全网最快的应助速度,最高的求助完成率。 对每一个文献求助,科研通都将尽心尽力,给求助人一个满意的交代。
实时播报
cowboy007发布了新的文献求助10
1秒前
乐乐应助eternity136采纳,获得10
2秒前
量子星尘发布了新的文献求助10
2秒前
3秒前
明眸完成签到 ,获得积分10
3秒前
4秒前
王手发布了新的文献求助10
5秒前
5秒前
5秒前
烟花应助zzq778采纳,获得10
7秒前
7秒前
欣欣发布了新的文献求助10
7秒前
小欣6116发布了新的文献求助10
8秒前
Jiuhui发布了新的文献求助10
8秒前
御风甜咖啡完成签到,获得积分10
8秒前
uupp完成签到,获得积分10
9秒前
机智雁凡完成签到,获得积分10
10秒前
Cheung2121发布了新的文献求助30
11秒前
12秒前
14秒前
谜记完成签到,获得积分10
14秒前
共享精神应助Cheung2121采纳,获得30
14秒前
光撒盐完成签到,获得积分10
15秒前
cowboy007完成签到,获得积分10
15秒前
张振宇完成签到 ,获得积分10
16秒前
zz发布了新的文献求助10
17秒前
zzq778发布了新的文献求助10
19秒前
黄怡婷完成签到 ,获得积分10
19秒前
Daisy应助科研通管家采纳,获得10
20秒前
机智苗应助科研通管家采纳,获得10
20秒前
香蕉觅云应助科研通管家采纳,获得10
20秒前
FashionBoy应助科研通管家采纳,获得10
20秒前
赘婿应助科研通管家采纳,获得10
20秒前
大模型应助科研通管家采纳,获得10
20秒前
yanmu2010应助科研通管家采纳,获得10
20秒前
kingwill应助科研通管家采纳,获得20
21秒前
银包铜应助科研通管家采纳,获得10
21秒前
共享精神应助科研通管家采纳,获得10
21秒前
21秒前
情怀应助科研通管家采纳,获得10
21秒前
高分求助中
【提示信息,请勿应助】关于scihub 10000
Les Mantodea de Guyane: Insecta, Polyneoptera [The Mantids of French Guiana] 3000
徐淮辽南地区新元古代叠层石及生物地层 3000
The Mother of All Tableaux: Order, Equivalence, and Geometry in the Large-scale Structure of Optimality Theory 3000
Global Eyelash Assessment scale (GEA) 1000
Picture Books with Same-sex Parented Families: Unintentional Censorship 550
Research on Disturbance Rejection Control Algorithm for Aerial Operation Robots 500
热门求助领域 (近24小时)
化学 材料科学 医学 生物 工程类 有机化学 生物化学 物理 内科学 纳米技术 计算机科学 化学工程 复合材料 遗传学 基因 物理化学 催化作用 冶金 细胞生物学 免疫学
热门帖子
关注 科研通微信公众号,转发送积分 4038368
求助须知:如何正确求助?哪些是违规求助? 3576068
关于积分的说明 11374313
捐赠科研通 3305780
什么是DOI,文献DOI怎么找? 1819322
邀请新用户注册赠送积分活动 892672
科研通“疑难数据库(出版商)”最低求助积分说明 815029